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- PDB-7avj: Streptococcal High Identity Repeats in Tandem (SHIRT) domain 2 fr... -

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Basic information

Entry
Database: PDB / ID: 7avj
TitleStreptococcal High Identity Repeats in Tandem (SHIRT) domain 2 from cell surface protein SGO_0707
ComponentsLPXTG cell wall surface protein
KeywordsCELL ADHESION / Bacterial surface / adhesin / tandem repeat / Sgo0707
Function / homology
Function and homology information


extracellular region / membrane
Similarity search - Function
SHIRT domain / Sgo0707, N-terminal domain / SHIRT domain / Sgo0707 N-terminal domain / Sgo0707-like, N2 domain / Sgo0707 N2 domain / Fimbrial isopeptide formation D2 domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
LPXTG cell wall surface protein
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.95 Å
AuthorsWhelan, F. / Jenkins, H.T. / Potts, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J005029/1 United Kingdom
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Periscope Proteins are variable-length regulators of bacterial cell surface interactions.
Authors: Whelan, F. / Lafita, A. / Gilburt, J. / Degut, C. / Griffiths, S.C. / Jenkins, H.T. / St John, A.N. / Paci, E. / Moir, J.W.B. / Plevin, M.J. / Baumann, C.G. / Bateman, A. / Potts, J.R.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Fragon: rapid high-resolution structure determination from ideal protein fragments.
Authors: Jenkins, H.T.
History
DepositionNov 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPXTG cell wall surface protein


Theoretical massNumber of molelcules
Total (without water)9,6271
Polymers9,6271
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)21.429, 40.766, 82.469
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LPXTG cell wall surface protein


Mass: 9627.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288) (bacteria)
Strain: Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288
Gene: SGO_0707 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8AW49
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7, 2.4 M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2014
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 0.95→82.48 Å / Num. obs: 44546 / % possible obs: 95.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 8.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Net I/σ(I): 24.8
Reflection shellResolution: 0.95→0.96 Å / Mean I/σ(I) obs: 2.29 / Num. unique obs: 2604 / CC1/2: 0.839 / % possible all: 75.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
Fragonphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.95→41.23 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.41 / SU ML: 0.01 / SU R Cruickshank DPI: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1329 2193 4.9 %RANDOM
Rwork0.1249 ---
obs0.1253 42240 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 167.49 Å2 / Biso mean: 15.717 Å2 / Biso min: 7.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.58 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 0.95→41.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms540 0 0 104 644
Biso mean---29.48 -
Num. residues----69
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02693
X-RAY DIFFRACTIONr_bond_other_d0.0020.02631
X-RAY DIFFRACTIONr_angle_refined_deg1.961.968965
X-RAY DIFFRACTIONr_angle_other_deg1.14731502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.153599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59626.29627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07815120
X-RAY DIFFRACTIONr_chiral_restr0.1280.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021810
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02138
X-RAY DIFFRACTIONr_mcbond_it1.8961.205341
X-RAY DIFFRACTIONr_mcbond_other1.8931.202340
X-RAY DIFFRACTIONr_mcangle_it2.8091.785440
X-RAY DIFFRACTIONr_rigid_bond_restr2.94331324
X-RAY DIFFRACTIONr_sphericity_free22.789549
X-RAY DIFFRACTIONr_sphericity_bonded12.1951344
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 146 -
Rwork0.247 2527 -
all-2673 -
obs--77.64 %

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